SMOG 2: A Versatile Software Package for Generating Structure-Based Models

dc.citation.journalTitlePLoS Computational Biologyen_US
dc.contributor.authorNoel, Jeffrey K.en_US
dc.contributor.authorLevi, Marianaen_US
dc.contributor.authorRaghunathan, Mohiten_US
dc.contributor.authorLammert, Heikoen_US
dc.contributor.authorHayes, Ryan L.en_US
dc.contributor.authorOnuchic, José N.en_US
dc.contributor.authorWhitford, Paul C.en_US
dc.contributor.orgCenter for Theoretical Biological Physicsen_US
dc.description.abstractMolecular dynamics simulations with coarse-grained or simplified Hamiltonians have proven to be an effective means of capturing the functionally important long-time and large-length scale motions of proteins and RNAs. Originally developed in the context of protein folding, structure-based models (SBMs) have since been extended to probe a diverse range of biomolecular processes, spanning from protein and RNA folding to functional transitions in molecular machines. The hallmark feature of a structure-based model is that part, or all, of the potential energy function is defined by a known structure. Within this general class of models, there exist many possible variations in resolution and energetic composition. SMOG 2 is a downloadable software package that reads user-designated structural information and user-defined energy definitions, in order to produce the files necessary to use SBMs with high performance molecular dynamics packages: GROMACS and NAMD. SMOG 2 is bundled with XML-formatted template files that define commonly used SBMs, and it can process template files that are altered according to the needs of each user. This computational infrastructure also allows for experimental or bioinformatics-derived restraints or novel structural features to be included, e.g. novel ligands, prosthetic groups and post-translational/transcriptional modifications. The code and user guide can be downloaded at
dc.identifier.citationNoel, Jeffrey K., Levi, Mariana, Raghunathan, Mohit, et al.. "SMOG 2: A Versatile Software Package for Generating Structure-Based Models." <i>PLoS Computational Biology,</i> 12, no. 3 (2016) Public Library of Science: e1004794.
dc.publisherPublic Library of Science
dc.rightsThis is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.en_US
dc.titleSMOG 2: A Versatile Software Package for Generating Structure-Based Modelsen_US
dc.typeJournal articleen_US
dc.type.publicationpublisher versionen_US
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